Yep, you need to get up in the night (if crate is shut) , don't worry that this will be a habit, as long as you go to them, no interaction, just pop them out into the garden, wee, poohs, once done, pop back in crate, you may need to get up a couple of times, our routine was:
To bed at 11 ish, set alarm for 2ish, then for around 5 ish, and gradually setting alarm 10 mins later, within about 3 - 4 weeks it was all running smoothly and dropped the two night times and went to bed at 11 and woke her up around 6. It does work. As others have said, she's bound to mess the crate if she has no other option.